The result of plink –freq is filled with NA
I downloaded the vcf file. Then I used plink to convert it to a bed file and calculated the array frequency.
However, the result of plink –freq was filled with NA.
Can anyone give us an opinion?
command
① ./plink –vcf ebi-a-GCST010775.vcf.gz –keep-allele-order –out covid –maf 0.2 –make-bed
② wc covid.*
0 1 9194292 covid.bed
9194289 55165734 262203653 covid.bim
1 6 43 covid.fam
30 146 1068 covid.log
③ ./plink –bfile covid –out COVID_1 –freq
④ head -n 5 COVID_1.frq
CHR SNP A1 A2 MAF NCHROBS
1 rs61769339 A G NA 0
1 rs12238997 G A NA 0
1 rs61769351 C G NA 0
1 rs144155419 A G NA 0
1 rs12565286 C G NA 0
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